title: CARPET: a web-based package for the analysis of ChIP-chip and expression tiling data.
abstract: CONCLUSIONS
  CARPET (collection of automated routine programs for easy tiling) is a set of Perl, Python and R scripts, integrated on the Galaxy2 web-based platform, for the analysis of ChIP-chip and expression tiling data, both for standard and custom chip designs. CARPET allows rapid experimental data entry, simple quality control, normalization, easy identification and annotation of enriched ChIP-chip regions, detection of the absolute or relative transcriptional status of genes assessed by expression tiling experiments and, more importantly, it allows the integration of ChIP-chip and expression data. Results can be visualized instantly in a genomic context within the UCSC genome browser as graph-based custom tracks through Galaxy2. All generated and uploaded data can be stored within sessions and are easily shared with other users.
  
  
  BACKGROUND
  http://bio.ifom-ieo-campus.it/galaxy
authors.affiliation: Department of Experimental Oncology, European Institute of Oncology, Via Ripamonti 435, 20141 Milano, Italy. matteo.cesaroni@ifom-ieo-campus.it
authors.forename: Matteo
authors.initials: M
authors.lastname: Cesaroni
authors.forename: Davide
authors.initials: D
authors.lastname: Cittaro
authors.forename: Alessandro
authors.initials: A
authors.lastname: Brozzi
authors.forename: Pier Giuseppe
authors.initials: PG
authors.lastname: Pelicci
authors.forename: Lucilla
authors.initials: L
authors.lastname: Luzi
mesh_terms: D047369:Chromatin Immunoprecipitation / Q000379:methods*; D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000379:methods*; D016678:Genome; D020407:Internet; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012984:Software; D014158:Transcription, Genetic